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Hi @cmsmith91 I am working on the response to reviewer regarding the random assignment of genera within families. For this, I wanted to **retrieve the names of those genera that were randomly assigned…
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Some pages have phylogenies. E.g. /occurrence/4527469336
That hasn't been implemented yet. Currently there is just a hello world stub that shows a tree. But styling is missing and it needs to load th…
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Sorry to bother you both @dan-knight @whelena !
I was trying to plot one emulsiphy result and got this error. I was wondering if this is an edge case with multiple root nodes, or it is something co…
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While doing integration testing at DARC, I ran into stability issues with Oni. Sometimes it would work fine, other times it would timeout waiting for a response from the database. This was most eviden…
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## Add probability column to input dataframe
Probability column can also be a p-value.
Probabilistic edge (connected to a node with multiple parents) should be different in colour or line type compa…
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I got a question from a user how to include a phylogenetic distance matrix. At some point we have to finally tackle this problem.
At the moment I can think of two options:
a) phylogenetic distance …
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Hi,
I'm trying to run on the example dataset using the command
`python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'`
with diamond version 4.0.515 and fasttree versio…
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Create phylogeny for each sample.
- [x] Create representative reference set to use as a whole genome backbone
- [x] Same for ompa gene only
- [ ] Create bed file of recombination regions to mask …
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salut, j'essaie de rouler phylophlan sur les noeuds et j'y arrive pas
avec ce script :
`/home/def-ilafores/analysis/boreal_moss/Phylogeny/phylophlan_slurm.sh
`
J'ai essayé avec et sans anchor en s…
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Hello,
We recently used TreeTime to infer ancestral sequences for a set of Influenza samples and then visualized the phylogenetic tree with the branches being annotated by the inferred mutations.
…